After some long thinking, I've finally come up with names for my protagonists.
Four letter names are assigned based on (planet/city) sector, facility, batch and individual. When someone does something truly outstanding for the empire, they earn the right to give themselves a new name.
Now I just need a name for their species as a whole...

Edit:
A kind anon suggested "Woozlesnoos" and I'm still laughing at it 10 minutes later, so I think this is it.